The adaptive immune system has the capacity to respond to a virtually limitless array of pathogens and environmental threats. The extensive molecular diversity required to recognize such varied targets is generated through the rearrangement and combinatorial association of antigen receptor gene segments in T and B lymphocytes. The DNA sequence of these variable gene segments determines the antigen specificity of encoded heterodimeric T cell receptors and B cell immunoglobulins. Although an immune response is not dictated by specificity alone, the antigen receptor serves as the principal site for lymphocyte recognition and engagement, directly linking this complex set of genetic information to functions in host defense, vaccination, and autoimmunity. Therefore, a comprehensive sequence inventory of the immunoglobulin and T cell receptor repertoire is a key step towards understanding, and perhaps manipulating, the adaptive immune response. However, determining the distinct sequences of diverse antigen receptor genes within a complex lymphocyte population presents a number of challenges, most notably in acquiring paired sequence information for both of the subunit chains that contribute to the specificity of th heterodimeric antigen receptor. The goal of this application is to develop a high throughput strategy that overcomes these challenges and enables sequence analysis of paired antigen receptor subunits. Using a combination of molecular biology, microfluidics technology, and high throughput sequencing, I will establish an effective method for rapidly profiling T cell receptor and B cell immunoglobulin sequences. This approach will be used for molecular and functional studies of the lymphocyte repertoire in the steady-state and in response to antigenic challenge. It will also be used to investigate the contribution of particular antigen receptor specificities t autoimmune pathogenesis in a model of systemic lupus erythematosus. These studies will significantly advance our understanding of the adaptive immune system in health and disease. Furthermore, the tools developed in this project will have broad utility for studying immune function in areas such as infection, vaccination, and autoimmunity. They can also be adapted for profiling complex populations at single cell resolution in a wide variety of biological systems